Pathway Analysis for FABIA & MOFA Ensembles
John Zhuang
2024-08-07
library(multiMiR)## Welcome to multiMiR.
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## multiMiR database URL has been set to the
## default value: http://multimir.org/
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## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan,
## X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal
## enrichment tool for interpreting omics data. The Innovation. 2021,
## 2(3):100141##
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## filterlibrary(org.Hs.eg.db)## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
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## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
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## select## library(stringr)
library(ggplot2)0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
results.superbiclust.fabia.mofa = readRDS("data/sel_features/results_superbiclust.fabia_mofa.rds")
sel.features = results.superbiclust.fabia.mofa$resNames
sel.features## [[1]]
## [1] "hsa-mir-1185-1" "hsa-mir-1197" "hsa-mir-127" "hsa-mir-134"
## [5] "hsa-mir-136" "hsa-mir-154" "hsa-mir-323" "hsa-mir-323b"
## [9] "hsa-mir-329-1" "hsa-mir-329-2" "hsa-mir-369" "hsa-mir-370"
## [13] "hsa-mir-376a-1" "hsa-mir-376a-2" "hsa-mir-376b" "hsa-mir-377"
## [17] "hsa-mir-380" "hsa-mir-382" "hsa-mir-410" "hsa-mir-432"
## [21] "hsa-mir-487a" "hsa-mir-487b" "hsa-mir-496" "hsa-mir-539"
## [25] "hsa-mir-541" "hsa-mir-654" "hsa-mir-655" "hsa-mir-656"
## [29] "hsa-mir-665" "hsa-mir-668" "hsa-mir-770" "hsa-mir-889"
##
## [[2]]
## [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-124-3" "hsa-mir-135b"
## [5] "hsa-mir-206" "hsa-mir-2114" "hsa-mir-3166" "hsa-mir-3199-1"
## [9] "hsa-mir-3655" "hsa-mir-3923" "hsa-mir-3926-2" "hsa-mir-411"
## [13] "hsa-mir-485" "hsa-mir-487a" "hsa-mir-494" "hsa-mir-506"
## [17] "hsa-mir-507" "hsa-mir-508" "hsa-mir-509-1" "hsa-mir-509-2"
## [21] "hsa-mir-509-3" "hsa-mir-510" "hsa-mir-513a-1" "hsa-mir-513a-2"
## [25] "hsa-mir-513b" "hsa-mir-513c" "hsa-mir-514-1" "hsa-mir-514-2"
## [29] "hsa-mir-514-3" "hsa-mir-514b" "hsa-mir-543" "hsa-mir-582"
##
## [[3]]
## [1] "TGM2.R2Gn" "hsa-mir-1185-1" "hsa-mir-329-1" "hsa-mir-329-2"
## [5] "hsa-mir-506" "hsa-mir-507" "hsa-mir-508" "hsa-mir-510"
## [9] "hsa-mir-513a-1" "hsa-mir-513a-2" "hsa-mir-513c" "hsa-mir-514b"
## [13] "hsa-mir-516b-1" "hsa-mir-517a" "hsa-mir-518b" "hsa-mir-656"
##
## [[4]]
## [1] "FASN.RPPA" "hsa-mir-3934" "hsa-mir-466" "hsa-mir-510" "hsa-mir-605"
##
## [[5]]
## character(0)
##
## [[6]]
## [1] "G6PD.RPPA"
##
## [[7]]
## [1] "G6PD.RPPA" "IGFBP2.RPPA" "RBM15.RPPA" "GATA3.RPPA" "PEA15.RPPA"
## [6] "ATM.RPPA" "INPP4B.RPPA" "ACVRL1.RPPA" "TSC1.RPPA" "CDK1.RPPA"
## [11] "VHL.RPPA" "PRDX1.RPPA" "XBP1.RPPA" "TFRC.RPPA" "PREX1.RPPA"
##
## [[8]]
## [1] "RBM15.RPPA" "EGFR.RPPA" "GAPDH.RPPA"
##
## [[9]]
## [1] "ANLN.R2Gn" "STMN1.R2Gn" "CDK1.R2Gn" "CCNB1.R2Gn" "FOXM1.R2Gn"
##
## [[10]]
## character(0)
##
## [[11]]
## character(0)
##
## [[12]]
## character(0)1. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
out = as.character(unique(out1))
out
}geneNames <- list("biclust1"=multiomics.to.GENES(sel.features[[1]]),
"biclust2"=multiomics.to.GENES(sel.features[[2]]),
"biclust3"=multiomics.to.GENES(sel.features[[3]]),
"biclust4"=multiomics.to.GENES(sel.features[[4]]),
"biclust6"=multiomics.to.GENES(sel.features[[6]]),
"biclust7"=multiomics.to.GENES(sel.features[[7]]),
"biclust8"=multiomics.to.GENES(sel.features[[8]]),
"biclust9"=multiomics.to.GENES(sel.features[[9]]))## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...geneNames## $biclust1
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "STAT5A" "CCND1" "YAP1" "MAPK1" "ANLN"
##
## $biclust2
## [1] "ESR1" "MET" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3" "AKT1"
## [9] "IGF1R" "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "PTEN" "NRAS"
## [17] "PTK2" "ATM" "YWHAZ" "FOXO3" "CHEK1" "FN1" "NCOA3" "GAB2"
## [25] "ITGA2"
##
## $biclust3
## [1] "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "NCOA3" "GAB2" "TGM2"
##
## $biclust4
## [1] "CCND1" "PIK3R1" "XIAP" "CHEK1" "IGF1R" "SRSF1" "TUBA1B" "FASN"
##
## $biclust6
## [1] "G6PD"
##
## $biclust7
## [1] "G6PD" "IGFBP2" "RBM15" "GATA3" "PEA15" "ATM" "INPP4B" "ACVRL1"
## [9] "TSC1" "CDK1" "VHL" "PRDX1" "XBP1" "TFRC" "PREX1"
##
## $biclust8
## [1] "RBM15" "EGFR" "GAPDH"
##
## $biclust9
## [1] "ANLN" "STMN1" "CDK1" "CCNB1" "FOXM1"saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_superbiclust.fabia_mofa.rds")2. Pathway Analysis
A. GO Classification
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/16
## GO:0003824 GO:0003824 catalytic activity 10 10/16
## GO:0005198 GO:0005198 structural molecule activity 0 0/16
## GO:0005215 GO:0005215 transporter activity 0 0/16
## GO:0005488 GO:0005488 binding 16 16/16
## GO:0009055 GO:0009055 electron transfer activity 0 0/16
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/CCND1/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 6 6/16
## GO:0002376 GO:0002376 immune system process 10 10/16
## GO:0008152 GO:0008152 metabolic process 15 15/16
## GO:0009987 GO:0009987 cellular process 16 16/16
## GO:0016032 GO:0016032 viral process 2 2/16
## GO:0022414 GO:0022414 reproductive process 6 6/16
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MAPK1
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
## GO:0016032 HSPA1A/AKT1
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 11 11/16
## GO:0044423 GO:0044423 virion component 0 0/16
## GO:0110165 GO:0110165 cellular anatomical entity 16 16/16
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/STAT5A/CCND1/YAP1
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/25
## GO:0003824 GO:0003824 catalytic activity 14 14/25
## GO:0005198 GO:0005198 structural molecule activity 1 1/25
## GO:0005215 GO:0005215 transporter activity 2 2/25
## GO:0005488 GO:0005488 binding 25 25/25
## GO:0009055 GO:0009055 electron transfer activity 0 0/25
## geneID
## GO:0003774
## GO:0003824 MET/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/MAPK8/PTEN/NRAS/PTK2/ATM/CHEK1/NCOA3
## GO:0005198 FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/25
## GO:0002376 GO:0002376 immune system process 17 17/25
## GO:0008152 GO:0008152 metabolic process 23 23/25
## GO:0009987 GO:0009987 cellular process 25 25/25
## GO:0016032 GO:0016032 viral process 3 3/25
## GO:0022414 GO:0022414 reproductive process 8 8/25
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/PTEN/ATM/FOXO3/ITGA2
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/FOXO3/FN1/GAB2/ITGA2
## GO:0008152 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/ITGA2
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2
## GO:0016032 BCL2/AKT1/ITGA2
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/PTEN/ATM/FOXO3/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 15 15/25
## GO:0044423 GO:0044423 virion component 0 0/25
## GO:0110165 GO:0110165 cellular anatomical entity 25 25/25
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/ETS1/ARID1A/ATM/FOXO3/CHEK1/FN1/NCOA3/ITGA2
## GO:0044423
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/8
## GO:0003824 GO:0003824 catalytic activity 4 4/8
## GO:0005198 GO:0005198 structural molecule activity 0 0/8
## GO:0005215 GO:0005215 transporter activity 0 0/8
## GO:0005488 GO:0005488 binding 8 8/8
## GO:0009055 GO:0009055 electron transfer activity 0 0/8
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/NCOA3/TGM2
## GO:0005198
## GO:0005215
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2/TGM2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/8
## GO:0002376 GO:0002376 immune system process 6 6/8
## GO:0008152 GO:0008152 metabolic process 7 7/8
## GO:0009987 GO:0009987 cellular process 8 8/8
## GO:0016032 GO:0016032 viral process 0 0/8
## GO:0022414 GO:0022414 reproductive process 0 0/8
## geneID
## GO:0000003
## GO:0002376 ETS1/XIAP/MAPK8/ARID1A/BID/GAB2
## GO:0008152 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/TGM2
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2/TGM2
## GO:0016032
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 4 4/8
## GO:0044423 GO:0044423 virion component 0 0/8
## GO:0110165 GO:0110165 cellular anatomical entity 8 8/8
## geneID
## GO:0032991 ETS1/ARID1A/NCOA3/TGM2
## GO:0044423
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2/TGM2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/8
## GO:0003824 GO:0003824 catalytic activity 7 7/8
## GO:0005198 GO:0005198 structural molecule activity 1 1/8
## GO:0005215 GO:0005215 transporter activity 1 1/8
## GO:0005488 GO:0005488 binding 8 8/8
## GO:0009055 GO:0009055 electron transfer activity 0 0/8
## geneID
## GO:0003774
## GO:0003824 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/TUBA1B/FASN
## GO:0005198 TUBA1B
## GO:0005215 IGF1R
## GO:0005488 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/FASN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/8
## GO:0002376 GO:0002376 immune system process 3 3/8
## GO:0008152 GO:0008152 metabolic process 7 7/8
## GO:0009987 GO:0009987 cellular process 8 8/8
## GO:0016032 GO:0016032 viral process 0 0/8
## GO:0022414 GO:0022414 reproductive process 1 1/8
## geneID
## GO:0000003 IGF1R
## GO:0002376 PIK3R1/XIAP/IGF1R
## GO:0008152 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/FASN
## GO:0009987 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/FASN
## GO:0016032
## GO:0022414 IGF1R
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 5 5/8
## GO:0044423 GO:0044423 virion component 0 0/8
## GO:0110165 GO:0110165 cellular anatomical entity 8 8/8
## geneID
## GO:0032991 CCND1/PIK3R1/CHEK1/IGF1R/SRSF1
## GO:0044423
## GO:0110165 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/FASN
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 1 1/1 G6PD
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 G6PD
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/1
## GO:0002376 GO:0002376 immune system process 1 1/1 G6PD
## GO:0008152 GO:0008152 metabolic process 1 1/1 G6PD
## GO:0009987 GO:0009987 cellular process 1 1/1 G6PD
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 0 0/1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 0 0/1
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 G6PD
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/15
## GO:0003824 GO:0003824 catalytic activity 7 7/15
## GO:0005198 GO:0005198 structural molecule activity 0 0/15
## GO:0005215 GO:0005215 transporter activity 0 0/15
## GO:0005488 GO:0005488 binding 15 15/15
## GO:0009055 GO:0009055 electron transfer activity 0 0/15
## geneID
## GO:0003774
## GO:0003824 G6PD/ATM/INPP4B/ACVRL1/CDK1/VHL/PRDX1
## GO:0005198
## GO:0005215
## GO:0005488 G6PD/IGFBP2/RBM15/GATA3/PEA15/ATM/INPP4B/ACVRL1/TSC1/CDK1/VHL/PRDX1/XBP1/TFRC/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 4 4/15
## GO:0002376 GO:0002376 immune system process 10 10/15
## GO:0008152 GO:0008152 metabolic process 13 13/15
## GO:0009987 GO:0009987 cellular process 15 15/15
## GO:0016032 GO:0016032 viral process 2 2/15
## GO:0022414 GO:0022414 reproductive process 4 4/15
## geneID
## GO:0000003 IGFBP2/GATA3/ATM/CDK1
## GO:0002376 G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/TFRC/PREX1
## GO:0008152 G6PD/RBM15/GATA3/ATM/INPP4B/ACVRL1/TSC1/CDK1/VHL/PRDX1/XBP1/TFRC/PREX1
## GO:0009987 G6PD/IGFBP2/RBM15/GATA3/PEA15/ATM/INPP4B/ACVRL1/TSC1/CDK1/VHL/PRDX1/XBP1/TFRC/PREX1
## GO:0016032 CDK1/TFRC
## GO:0022414 IGFBP2/GATA3/ATM/CDK1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 9 9/15
## GO:0044423 GO:0044423 virion component 0 0/15
## GO:0110165 GO:0110165 cellular anatomical entity 15 15/15
## geneID
## GO:0032991 RBM15/GATA3/PEA15/ATM/ACVRL1/TSC1/CDK1/XBP1/TFRC
## GO:0044423
## GO:0110165 G6PD/IGFBP2/RBM15/GATA3/PEA15/ATM/INPP4B/ACVRL1/TSC1/CDK1/VHL/PRDX1/XBP1/TFRC/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/3
## GO:0003824 GO:0003824 catalytic activity 2 2/3
## GO:0005198 GO:0005198 structural molecule activity 0 0/3
## GO:0005215 GO:0005215 transporter activity 0 0/3
## GO:0005488 GO:0005488 binding 3 3/3
## GO:0009055 GO:0009055 electron transfer activity 0 0/3
## geneID
## GO:0003774
## GO:0003824 EGFR/GAPDH
## GO:0005198
## GO:0005215
## GO:0005488 RBM15/EGFR/GAPDH
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 1 1/3 EGFR
## GO:0002376 GO:0002376 immune system process 2 2/3 RBM15/GAPDH
## GO:0008152 GO:0008152 metabolic process 3 3/3 RBM15/EGFR/GAPDH
## GO:0009987 GO:0009987 cellular process 3 3/3 RBM15/EGFR/GAPDH
## GO:0016032 GO:0016032 viral process 1 1/3 EGFR
## GO:0022414 GO:0022414 reproductive process 1 1/3 EGFR
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/3
## GO:0044423 GO:0044423 virion component 0 0/3
## GO:0110165 GO:0110165 cellular anatomical entity 3 3/3
## geneID
## GO:0032991 RBM15/EGFR/GAPDH
## GO:0044423
## GO:0110165 RBM15/EGFR/GAPDH
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/5
## GO:0003824 GO:0003824 catalytic activity 1 1/5
## GO:0005198 GO:0005198 structural molecule activity 0 0/5
## GO:0005215 GO:0005215 transporter activity 0 0/5
## GO:0005488 GO:0005488 binding 5 5/5
## GO:0009055 GO:0009055 electron transfer activity 0 0/5
## geneID
## GO:0003774
## GO:0003824 CDK1
## GO:0005198
## GO:0005215
## GO:0005488 ANLN/STMN1/CDK1/CCNB1/FOXM1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/5
## GO:0002376 GO:0002376 immune system process 0 0/5
## GO:0008152 GO:0008152 metabolic process 3 3/5
## GO:0009987 GO:0009987 cellular process 5 5/5
## GO:0016032 GO:0016032 viral process 1 1/5
## GO:0022414 GO:0022414 reproductive process 1 1/5
## geneID
## GO:0000003 CDK1
## GO:0002376
## GO:0008152 CDK1/CCNB1/FOXM1
## GO:0009987 ANLN/STMN1/CDK1/CCNB1/FOXM1
## GO:0016032 CDK1
## GO:0022414 CDK1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/5
## GO:0044423 GO:0044423 virion component 0 0/5
## GO:0110165 GO:0110165 cellular anatomical entity 5 5/5
## geneID
## GO:0032991 CDK1/CCNB1/FOXM1
## GO:0044423
## GO:0110165 ANLN/STMN1/CDK1/CCNB1/FOXM1barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, bicluster 1")
barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, bicluster 2")
barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, bicluster 3")
barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, bicluster 4")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, bicluster 6")
barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, bicluster 7")
barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, bicluster 8")
barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, bicluster 9")
barplot(ggo_BP[[1]], title = "groupGO, Biological Process, bicluster 1")
barplot(ggo_BP[[2]], title = "groupGO, Biological Process, bicluster 2")
barplot(ggo_BP[[3]], title = "groupGO, Biological Process, bicluster 3")
barplot(ggo_BP[[4]], title = "groupGO, Biological Process, bicluster 4")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, bicluster 6")
barplot(ggo_BP[[6]], title = "groupGO, Biological Process, bicluster 7")
barplot(ggo_BP[[7]], title = "groupGO, Biological Process, bicluster 8")
barplot(ggo_BP[[8]], title = "groupGO, Biological Process, bicluster 9")
barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, bicluster 1")
barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, bicluster 2")
barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, bicluster 3")
barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, bicluster 4")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, bicluster 6")
barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, bicluster 7")
barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, bicluster 8")
barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, bicluster 9")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8for(z in 1:length(geneNames)){
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID Description
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0004707 GO:0004707 MAP kinase activity
## GO:0070064 GO:0070064 proline-rich region binding
## GO:0042826 GO:0042826 histone deacetylase binding
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0106310 5/16 363/18522 1.028418e-05 0.001244385 0.0004330180
## GO:0004674 5/16 427/18522 2.252414e-05 0.001362710 0.0004741923
## GO:0004707 2/16 16/18522 8.336346e-05 0.002856537 0.0009940104
## GO:0070064 2/16 17/18522 9.443099e-05 0.002856537 0.0009940104
## GO:0042826 3/16 128/18522 1.690349e-04 0.004090645 0.0014234520
## GO:0030291 2/16 37/18522 4.577980e-04 0.009232259 0.0032126172
## geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## GO:0030291 AKT1/CDKN1A 2
## ID Description GeneRatio
## GO:0062197 GO:0062197 cellular response to chemical stress 7/16
## GO:0009408 GO:0009408 response to heat 5/16
## GO:0034599 GO:0034599 cellular response to oxidative stress 6/16
## GO:0034198 GO:0034198 cellular response to amino acid starvation 4/16
## GO:1990928 GO:1990928 response to amino acid starvation 4/16
## GO:0034614 GO:0034614 cellular response to reactive oxygen species 5/16
## BgRatio pvalue p.adjust qvalue
## GO:0062197 311/18888 3.090160e-09 5.185288e-06 1.876866e-06
## GO:0009408 104/18888 1.911902e-08 1.604086e-05 5.806146e-06
## GO:0034599 248/18888 3.459920e-08 1.935249e-05 7.004821e-06
## GO:0034198 51/18888 8.376414e-08 3.337785e-05 1.208144e-05
## GO:1990928 54/18888 1.058426e-07 3.337785e-05 1.208144e-05
## GO:0034614 151/18888 1.243248e-07 3.337785e-05 1.208144e-05
## geneID Count
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1 7
## GO:0009408 HSPA1A/AKT1/MTOR/CDKN1A/ATM 5
## GO:0034599 HSPA1A/AKT1/MAPK8/FOXO3/ATM/MAPK1 6
## GO:0034198 MTOR/MAPK8/CDKN1A/MAPK1 4
## GO:1990928 MTOR/MAPK8/CDKN1A/MAPK1 4
## GO:0034614 AKT1/MAPK8/FOXO3/ATM/MAPK1 5
## ID Description
## GO:0005826 GO:0005826 actomyosin contractile ring
## GO:0070938 GO:0070938 contractile ring
## GO:0005819 GO:0005819 spindle
## GO:0008180 GO:0008180 COP9 signalosome
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005826 2/16 4/19894 3.635235e-06 0.0003635235 0.0001913281
## GO:0070938 2/16 10/19894 2.718760e-05 0.0013593802 0.0007154633
## GO:0005819 4/16 433/19894 3.272457e-04 0.0094003057 0.0049475293
## GO:0008180 2/16 36/19894 3.760122e-04 0.0094003057 0.0049475293
## GO:0005741 3/16 219/19894 6.628567e-04 0.0121604395 0.0064002313
## GO:0000307 2/16 56/19894 9.105620e-04 0.0121604395 0.0064002313
## geneID Count
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0005819 AKT1/MYH9/ATM/MAPK1 4
## GO:0008180 HSPA1A/MYH9 2
## GO:0005741 MTOR/FOXO3/CASP8 3
## GO:0000307 CDKN1A/CCND1 2
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 6/25
## GO:0030235 GO:0030235 nitric-oxide synthase regulator activity 2/25
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/25
## GO:0019903 GO:0019903 protein phosphatase binding 4/25
## GO:0019902 GO:0019902 phosphatase binding 4/25
## GO:0035173 GO:0035173 histone kinase activity 2/25
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 3.340010e-05 0.001894097 0.0008850464
## GO:0030235 7/18522 3.657799e-05 0.001894097 0.0008850464
## GO:0120283 7/18522 3.657799e-05 0.001894097 0.0008850464
## GO:0019903 142/18522 3.695798e-05 0.001894097 0.0008850464
## GO:0019902 189/18522 1.123278e-04 0.004605439 0.0021519640
## GO:0035173 23/18522 4.348808e-04 0.013856762 0.0064747897
## geneID Count
## GO:0140297 ESR1/BCL2/ETS1/ARID1A/YWHAZ/NCOA3 6
## GO:0030235 ESR1/AKT1 2
## GO:0120283 XIAP/MAPK8 2
## GO:0019903 MET/BCL2/MAPK8/PTK2 4
## GO:0019902 MET/BCL2/MAPK8/PTK2 4
## GO:0035173 ATM/CHEK1 2
## ID Description
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806 regulation of cell cycle G1/S phase transition
## GO:1901990 GO:1901990 regulation of mitotic cell cycle phase transition
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843 cell cycle G1/S phase transition
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051402 8/25 292/18888 2.552612e-09 3.162876e-06 1.382880e-06
## GO:2000045 7/25 185/18888 3.196439e-09 3.162876e-06 1.382880e-06
## GO:1902806 7/25 211/18888 7.964698e-09 5.254046e-06 2.297187e-06
## GO:1901990 8/25 356/18888 1.203946e-08 5.956522e-06 2.604325e-06
## GO:0000082 7/25 234/18888 1.627946e-08 6.443412e-06 2.817204e-06
## GO:0044843 7/25 262/18888 3.541992e-08 1.168267e-05 5.107926e-06
## geneID Count
## GO:0051402 G6PD/BCL2/KRAS/CCND1/XIAP/BID/ATM/FOXO3 8
## GO:2000045 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM 7
## GO:1902806 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM 7
## GO:1901990 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM/CHEK1 8
## GO:0000082 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM 7
## GO:0044843 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM 7
## ID Description GeneRatio BgRatio
## GO:0005741 GO:0005741 mitochondrial outer membrane 4/25 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 4/25 248/19894
## GO:0019867 GO:0019867 outer membrane 4/25 250/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane 3/25 161/19894
## GO:0043209 GO:0043209 myelin sheath 2/25 46/19894
## GO:0005925 GO:0005925 focal adhesion 4/25 421/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005741 0.0001507289 0.008506653 0.005794005 BCL2/KRAS/BID/FOXO3 4
## GO:0031968 0.0002426479 0.008506653 0.005794005 BCL2/KRAS/BID/FOXO3 4
## GO:0019867 0.0002501957 0.008506653 0.005794005 BCL2/KRAS/BID/FOXO3 4
## GO:0009898 0.0010497787 0.024580717 0.016742284 G6PD/KRAS/PTEN 3
## GO:0043209 0.0015168846 0.024580717 0.016742284 BCL2/PTEN 2
## GO:0005925 0.0017581642 0.024580717 0.016742284 KRAS/PTK2/YWHAZ/ITGA2 4
## ID
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0030374 GO:0030374
## GO:0061629 GO:0061629
## GO:0016410 GO:0016410
## GO:0140297 GO:0140297
## Description
## GO:0120283 protein serine/threonine kinase binding
## GO:0003713 transcription coactivator activity
## GO:0030374 nuclear receptor coactivator activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0016410 N-acyltransferase activity
## GO:0140297 DNA-binding transcription factor binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0120283 2/8 7/18522 3.424411e-06 0.000232860 9.732538e-05
## GO:0003713 3/8 271/18522 1.642917e-04 0.005432205 2.270426e-03
## GO:0030374 2/8 55/18522 2.396561e-04 0.005432205 2.270426e-03
## GO:0061629 3/8 343/18522 3.290146e-04 0.005593248 2.337735e-03
## GO:0016410 2/8 95/18522 7.143770e-04 0.009715527 4.060669e-03
## GO:0140297 3/8 478/18522 8.683135e-04 0.009840887 4.113064e-03
## geneID Count
## GO:0120283 XIAP/MAPK8 2
## GO:0003713 ETS1/ARID1A/NCOA3 3
## GO:0030374 ETS1/NCOA3 2
## GO:0061629 ETS1/ARID1A/NCOA3 3
## GO:0016410 NCOA3/TGM2 2
## GO:0140297 ETS1/ARID1A/NCOA3 3
## ID Description
## GO:1902459 GO:1902459 positive regulation of stem cell population maintenance
## GO:0030522 GO:0030522 intracellular receptor signaling pathway
## GO:2000036 GO:2000036 regulation of stem cell population maintenance
## GO:0018277 GO:0018277 protein deamination
## GO:1902528 GO:1902528 regulation of protein linear polyubiquitination
## GO:1902530 GO:1902530 positive regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1902459 2/8 48/18888 0.0001753538 0.04414629 0.02178271
## GO:0030522 3/8 369/18888 0.0003850393 0.04414629 0.02178271
## GO:2000036 2/8 73/18888 0.0004063778 0.04414629 0.02178271
## GO:0018277 1/8 2/18888 0.0008469417 0.04414629 0.02178271
## GO:1902528 1/8 2/18888 0.0008469417 0.04414629 0.02178271
## GO:1902530 1/8 2/18888 0.0008469417 0.04414629 0.02178271
## geneID Count
## GO:1902459 ARID1A/NCOA3 2
## GO:0030522 XIAP/MAPK8/ARID1A 3
## GO:2000036 ARID1A/NCOA3 2
## GO:0018277 TGM2 1
## GO:1902528 XIAP 1
## GO:1902530 XIAP 1
## ID Description GeneRatio BgRatio pvalue p.adjust
## GO:0097441 GO:0097441 basal dendrite 1/8 6/19894 0.002410666 0.02181829
## GO:0140092 GO:0140092 bBAF complex 1/8 10/19894 0.004014950 0.02181829
## GO:0035060 GO:0035060 brahma complex 1/8 14/19894 0.005616977 0.02181829
## GO:0071564 GO:0071564 npBAF complex 1/8 14/19894 0.005616977 0.02181829
## GO:0071565 GO:0071565 nBAF complex 1/8 16/19894 0.006417144 0.02181829
## GO:0016514 GO:0016514 SWI/SNF complex 1/8 30/19894 0.012002558 0.03400725
## qvalue geneID Count
## GO:0097441 0.01350978 MAPK8 1
## GO:0140092 0.01350978 ARID1A 1
## GO:0035060 0.01350978 ARID1A 1
## GO:0071564 0.01350978 ARID1A 1
## GO:0071565 0.01350978 ARID1A 1
## GO:0016514 0.02105712 ARID1A 1
## ID Description GeneRatio BgRatio
## GO:0043559 GO:0043559 insulin binding 2/8 5/18522
## GO:0043560 GO:0043560 insulin receptor substrate binding 2/8 13/18522
## GO:0005158 GO:0005158 insulin receptor binding 2/8 22/18522
## GO:0043548 GO:0043548 phosphatidylinositol 3-kinase binding 2/8 25/18522
## GO:0017046 GO:0017046 peptide hormone binding 2/8 50/18522
## GO:0033218 GO:0033218 amide binding 3/8 409/18522
## pvalue p.adjust qvalue geneID Count
## GO:0043559 1.631377e-06 0.0001761887 6.182059e-05 PIK3R1/IGF1R 2
## GO:0043560 1.270277e-05 0.0006859494 2.406840e-04 PIK3R1/IGF1R 2
## GO:0005158 3.754665e-05 0.0013157179 4.616554e-04 PIK3R1/IGF1R 2
## GO:0043548 4.873029e-05 0.0013157179 4.616554e-04 PIK3R1/IGF1R 2
## GO:0017046 1.979099e-04 0.0042748535 1.499949e-03 PIK3R1/IGF1R 2
## GO:0033218 5.511240e-04 0.0049093069 1.722564e-03 PIK3R1/IGF1R/FASN 3
## ID Description
## GO:0031099 GO:0031099 regeneration
## GO:0097421 GO:0097421 liver regeneration
## GO:0071353 GO:0071353 cellular response to interleukin-4
## GO:0070670 GO:0070670 response to interleukin-4
## GO:0033120 GO:0033120 positive regulation of RNA splicing
## GO:0048009 GO:0048009 insulin-like growth factor receptor signaling pathway
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031099 3/8 200/18888 6.298081e-05 0.01533276 0.006745377
## GO:0097421 2/8 30/18888 6.788160e-05 0.01533276 0.006745377
## GO:0071353 2/8 34/18888 8.746969e-05 0.01533276 0.006745377
## GO:0070670 2/8 37/18888 1.037750e-04 0.01533276 0.006745377
## GO:0033120 2/8 50/18888 1.903523e-04 0.01886635 0.008299917
## GO:0048009 2/8 53/18888 2.139908e-04 0.01886635 0.008299917
## geneID Count
## GO:0031099 CCND1/IGF1R/SRSF1 3
## GO:0097421 CCND1/SRSF1 2
## GO:0071353 TUBA1B/FASN 2
## GO:0070670 TUBA1B/FASN 2
## GO:0033120 PIK3R1/SRSF1 2
## GO:0048009 PIK3R1/IGF1R 2
## ID
## GO:0061695 GO:0061695
## GO:0097128 GO:0097128
## GO:1902911 GO:1902911
## GO:0005899 GO:0005899
## GO:0035867 GO:0035867
## GO:1990578 GO:1990578
## Description
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0097128 cyclin D1-CDK4 complex
## GO:1902911 protein kinase complex
## GO:0005899 insulin receptor complex
## GO:0035867 alphav-beta3 integrin-IGF-1-IGF1R complex
## GO:1990578 perinuclear endoplasmic reticulum membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0061695 3/8 308/19894 0.0001942755 0.008353845 0.003681009
## GO:0097128 1/8 2/19894 0.0008041211 0.011521680 0.005076873
## GO:1902911 2/8 150/19894 0.0015348825 0.011521680 0.005076873
## GO:0005899 1/8 4/19894 0.0016076763 0.011521680 0.005076873
## GO:0035867 1/8 4/19894 0.0016076763 0.011521680 0.005076873
## GO:1990578 1/8 4/19894 0.0016076763 0.011521680 0.005076873
## geneID Count
## GO:0061695 CCND1/PIK3R1/IGF1R 3
## GO:0097128 CCND1 1
## GO:1902911 CCND1/IGF1R 2
## GO:0005899 IGF1R 1
## GO:0035867 IGF1R 1
## GO:1990578 PIK3R1 1
## ID
## GO:0004345 GO:0004345
## GO:0005536 GO:0005536
## GO:0050661 GO:0050661
## GO:0048029 GO:0048029
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## Description
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GO:0005536 glucose binding
## GO:0050661 NADP binding
## GO:0048029 monosaccharide binding
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004345 1/1 2/18522 0.0001079797 0.0007558579 NA G6PD 1
## GO:0005536 1/1 11/18522 0.0005938883 0.0020786092 NA G6PD 1
## GO:0050661 1/1 53/18522 0.0028614620 0.0066767448 NA G6PD 1
## GO:0048029 1/1 74/18522 0.0039952489 0.0069916856 NA G6PD 1
## GO:0016616 1/1 125/18522 0.0067487312 0.0085034014 NA G6PD 1
## GO:0016614 1/1 135/18522 0.0072886297 0.0085034014 NA G6PD 1
## ID
## GO:0010731 GO:0010731
## GO:0010732 GO:0010732
## GO:0010734 GO:0010734
## GO:0019322 GO:0019322
## GO:1904879 GO:1904879
## GO:0009051 GO:0009051
## Description
## GO:0010731 protein glutathionylation
## GO:0010732 regulation of protein glutathionylation
## GO:0010734 negative regulation of protein glutathionylation
## GO:0019322 pentose biosynthetic process
## GO:1904879 positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel
## GO:0009051 pentose-phosphate shunt, oxidative branch
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0010731 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0010732 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0010734 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0019322 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:1904879 1/1 3/18888 0.0001588310 0.003872451 NA G6PD 1
## GO:0009051 1/1 4/18888 0.0002117747 0.003872451 NA G6PD 1
## ID Description GeneRatio BgRatio
## GO:0034451 GO:0034451 centriolar satellite 1/1 126/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane 1/1 161/19894
## GO:0098562 GO:0098562 cytoplasmic side of membrane 1/1 199/19894
## pvalue p.adjust qvalue geneID Count
## GO:0034451 0.006333568 0.01000302 NA G6PD 1
## GO:0009898 0.008092892 0.01000302 NA G6PD 1
## GO:0098562 0.010003016 0.01000302 NA G6PD 1
## ID Description GeneRatio
## GO:0030544 GO:0030544 Hsp70 protein binding 3/15
## GO:0031072 GO:0031072 heat shock protein binding 3/15
## GO:0035173 GO:0035173 histone kinase activity 2/15
## GO:0051087 GO:0051087 protein-folding chaperone binding 3/15
## GO:0004345 GO:0004345 glucose-6-phosphate dehydrogenase activity 1/15
## GO:0004998 GO:0004998 transferrin receptor activity 1/15
## BgRatio pvalue p.adjust qvalue geneID
## GO:0030544 51/18522 8.742153e-06 0.0008042781 0.0002944725 TSC1/CDK1/TFRC
## GO:0031072 130/18522 1.445214e-04 0.0035561457 0.0013020213 TSC1/CDK1/TFRC
## GO:0035173 23/18522 1.533626e-04 0.0035561457 0.0013020213 ATM/CDK1
## GO:0051087 133/18522 1.546150e-04 0.0035561457 0.0013020213 TSC1/CDK1/TFRC
## GO:0004345 2/18522 1.619083e-03 0.0155992780 0.0057114061 G6PD
## GO:0004998 2/18522 1.619083e-03 0.0155992780 0.0057114061 TFRC
## Count
## GO:0030544 3
## GO:0031072 3
## GO:0035173 2
## GO:0051087 3
## GO:0004345 1
## GO:0004998 1
## ID Description GeneRatio
## GO:0045785 GO:0045785 positive regulation of cell adhesion 7/15
## GO:0036293 GO:0036293 response to decreased oxygen levels 5/15
## GO:0070482 GO:0070482 response to oxygen levels 5/15
## GO:1904262 GO:1904262 negative regulation of TORC1 signaling 3/15
## GO:0031929 GO:0031929 TOR signaling 4/15
## GO:0002520 GO:0002520 immune system development 4/15
## BgRatio pvalue p.adjust qvalue
## GO:0045785 485/18888 3.795691e-08 4.957173e-05 2.305383e-05
## GO:0036293 327/18888 3.928245e-06 1.857270e-03 8.637421e-04
## GO:0070482 354/18888 5.784493e-06 1.857270e-03 8.637421e-04
## GO:1904262 47/18888 6.433980e-06 1.857270e-03 8.637421e-04
## GO:0031929 165/18888 7.110528e-06 1.857270e-03 8.637421e-04
## GO:0002520 197/18888 1.431938e-05 2.835323e-03 1.318595e-03
## geneID Count
## GO:0045785 IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC/PREX1 7
## GO:0036293 ATM/ACVRL1/TSC1/VHL/TFRC 5
## GO:0070482 ATM/ACVRL1/TSC1/VHL/TFRC 5
## GO:1904262 ATM/TSC1/VHL 3
## GO:0031929 GATA3/ATM/TSC1/VHL 4
## GO:0002520 RBM15/GATA3/ATM/TFRC 4
## ID Description GeneRatio BgRatio pvalue
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex 1/15 2/19894 0.001507462
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 1/15 2/19894 0.001507462
## GO:0033596 GO:0033596 TSC1-TSC2 complex 1/15 4/19894 0.003012802
## GO:0070724 GO:0070724 BMP receptor complex 1/15 4/19894 0.003012802
## GO:0042470 GO:0042470 melanosome 2/15 112/19894 0.003144193
## GO:0048770 GO:0048770 pigment granule 2/15 112/19894 0.003144193
## p.adjust qvalue geneID Count
## GO:0097122 0.03825434 0.02978709 CDK1 1
## GO:0097125 0.03825434 0.02978709 CDK1 1
## GO:0033596 0.03825434 0.02978709 TSC1 1
## GO:0070724 0.03825434 0.02978709 ACVRL1 1
## GO:0042470 0.03825434 0.02978709 PRDX1/TFRC 2
## GO:0048770 0.03825434 0.02978709 PRDX1/TFRC 2
## ID
## GO:0004365 GO:0004365
## GO:0043891 GO:0043891
## GO:0005006 GO:0005006
## GO:0048408 GO:0048408
## GO:0030235 GO:0030235
## GO:0019828 GO:0019828
## Description
## GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
## GO:0043891 glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity
## GO:0005006 epidermal growth factor receptor activity
## GO:0048408 epidermal growth factor binding
## GO:0030235 nitric-oxide synthase regulator activity
## GO:0019828 aspartic-type endopeptidase inhibitor activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004365 1/3 2/18522 0.0003239216 0.007125506 0.001022800 GAPDH 1
## GO:0043891 1/3 2/18522 0.0003239216 0.007125506 0.001022800 GAPDH 1
## GO:0005006 1/3 3/18522 0.0004858562 0.007125506 0.001022800 EGFR 1
## GO:0048408 1/3 4/18522 0.0006477733 0.007125506 0.001022800 EGFR 1
## GO:0030235 1/3 7/18522 0.0011334196 0.009498623 0.001363439 EGFR 1
## GO:0019828 1/3 8/18522 0.0012952667 0.009498623 0.001363439 GAPDH 1
## ID
## GO:0001890 GO:0001890
## GO:0035606 GO:0035606
## GO:1902722 GO:1902722
## GO:0033590 GO:0033590
## GO:0033594 GO:0033594
## GO:0010750 GO:0010750
## Description
## GO:0001890 placenta development
## GO:0035606 peptidyl-cysteine S-trans-nitrosylation
## GO:1902722 positive regulation of prolactin secretion
## GO:0033590 response to cobalamin
## GO:0033594 response to hydroxyisoflavone
## GO:0010750 positive regulation of nitric oxide mediated signal transduction
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0001890 2/3 150/18888 0.0001869713 0.0292701 0.005275792 RBM15/EGFR
## GO:0035606 1/3 2/18888 0.0003176452 0.0292701 0.005275792 GAPDH
## GO:1902722 1/3 2/18888 0.0003176452 0.0292701 0.005275792 EGFR
## GO:0033590 1/3 4/18888 0.0006352231 0.0292701 0.005275792 EGFR
## GO:0033594 1/3 4/18888 0.0006352231 0.0292701 0.005275792 EGFR
## GO:0010750 1/3 5/18888 0.0007939868 0.0292701 0.005275792 EGFR
## Count
## GO:0001890 2
## GO:0035606 1
## GO:1902722 1
## GO:0033590 1
## GO:0033594 1
## GO:0010750 1
## ID Description
## GO:0031965 GO:0031965 nuclear membrane
## GO:0005635 GO:0005635 nuclear envelope
## GO:0070435 GO:0070435 Shc-EGFR complex
## GO:0097452 GO:0097452 GAIT complex
## GO:0097487 GO:0097487 multivesicular body, internal vesicle
## GO:0036396 GO:0036396 RNA N6-methyladenosine methyltransferase complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031965 3/3 313/19894 3.857967e-06 0.0001427448 3.654916e-05
## GO:0005635 3/3 498/19894 1.559432e-05 0.0002884950 7.386785e-05
## GO:0070435 1/3 2/19894 3.015833e-04 0.0037195275 9.523684e-04
## GO:0097452 1/3 4/19894 6.031060e-04 0.0055787303 1.428409e-03
## GO:0097487 1/3 6/19894 9.045680e-04 0.0066938033 1.713918e-03
## GO:0036396 1/3 9/19894 1.356647e-03 0.0083659922 2.142075e-03
## geneID Count
## GO:0031965 RBM15/EGFR/GAPDH 3
## GO:0005635 RBM15/EGFR/GAPDH 3
## GO:0070435 EGFR 1
## GO:0097452 GAPDH 1
## GO:0097487 EGFR 1
## GO:0036396 RBM15 1
## ID
## GO:0005113 GO:0005113
## GO:0008353 GO:0008353
## GO:0061575 GO:0061575
## GO:0035173 GO:0035173
## GO:0140994 GO:0140994
## GO:0004693 GO:0004693
## Description
## GO:0005113 patched binding
## GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity
## GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity
## GO:0035173 histone kinase activity
## GO:0140994 RNA polymerase II CTD heptapeptide repeat modifying activity
## GO:0004693 cyclin-dependent protein serine/threonine kinase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0005113 1/5 8/18522 0.002157962 0.0289896 0.01056301 CCNB1 1
## GO:0008353 1/5 10/18522 0.002696870 0.0289896 0.01056301 CDK1 1
## GO:0061575 1/5 16/18522 0.004312197 0.0289896 0.01056301 CCNB1 1
## GO:0035173 1/5 23/18522 0.006194099 0.0289896 0.01056301 CDK1 1
## GO:0140994 1/5 23/18522 0.006194099 0.0289896 0.01056301 CDK1 1
## GO:0004693 1/5 29/18522 0.007804892 0.0289896 0.01056301 CDK1 1
## ID
## GO:1905448 GO:1905448
## GO:1905446 GO:1905446
## GO:0044772 GO:0044772
## GO:0000086 GO:0000086
## GO:0044839 GO:0044839
## GO:1902850 GO:1902850
## Description
## GO:1905448 positive regulation of mitochondrial ATP synthesis coupled electron transport
## GO:1905446 regulation of mitochondrial ATP synthesis coupled electron transport
## GO:0044772 mitotic cell cycle phase transition
## GO:0000086 G2/M transition of mitotic cell cycle
## GO:0044839 cell cycle G2/M phase transition
## GO:1902850 microtubule cytoskeleton organization involved in mitosis
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1905448 2/5 4/18888 3.363104e-07 0.0001069467 2.584280e-05
## GO:1905446 2/5 7/18888 1.176712e-06 0.0001668324 4.031369e-05
## GO:0044772 4/5 451/18888 1.573891e-06 0.0001668324 4.031369e-05
## GO:0000086 3/5 136/18888 3.613177e-06 0.0002872476 6.941103e-05
## GO:0044839 3/5 152/18888 5.049737e-06 0.0003211632 7.760648e-05
## GO:1902850 3/5 164/18888 6.345810e-06 0.0003363279 8.127090e-05
## geneID Count
## GO:1905448 CDK1/CCNB1 2
## GO:1905446 CDK1/CCNB1 2
## GO:0044772 ANLN/CDK1/CCNB1/FOXM1 4
## GO:0000086 CDK1/CCNB1/FOXM1 3
## GO:0044839 CDK1/CCNB1/FOXM1 3
## GO:1902850 STMN1/CDK1/CCNB1 3
## ID Description
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex
## GO:1902911 GO:1902911 protein kinase complex
## GO:0005826 GO:0005826 actomyosin contractile ring
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0097125 2/5 2/19894 5.053678e-08 1.364493e-06 1.595898e-07
## GO:0000307 2/5 56/19894 7.740495e-05 1.044967e-03 1.222183e-04
## GO:1902554 2/5 136/19894 4.577086e-04 3.004513e-03 3.514051e-04
## GO:0097122 1/5 2/19894 5.026136e-04 3.004513e-03 3.514051e-04
## GO:1902911 2/5 150/19894 5.563914e-04 3.004513e-03 3.514051e-04
## GO:0005826 1/5 4/19894 1.005025e-03 3.993377e-03 4.670617e-04
## geneID Count
## GO:0097125 CDK1/CCNB1 2
## GO:0000307 CDK1/CCNB1 2
## GO:1902554 CDK1/CCNB1 2
## GO:0097122 CDK1 1
## GO:1902911 CDK1/CCNB1 2
## GO:0005826 ANLN 1barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, bicluster 1")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, bicluster 2")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, bicluster 3")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, bicluster 4")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, bicluster 6")
barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, bicluster 7")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, bicluster 8")
barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, bicluster 9")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, bicluster 1")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, bicluster 2")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, bicluster 3")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, bicluster 4")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, bicluster 6")
barplot(ego_BP[[6]], title = "enrichGO, Biological Process, bicluster 7")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, bicluster 8")
barplot(ego_BP[[8]], title = "enrichGO, Biological Process, bicluster 9")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, bicluster 1")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, bicluster 2")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, bicluster 3")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, bicluster 4")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, bicluster 6")
barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, bicluster 7")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, bicluster 8")
barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, bicluster 9")
DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, bicluster 1")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, bicluster 2")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, bicluster 3")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, bicluster 4")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, bicluster 6")
goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, bicluster 7")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, bicluster 8")
goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, bicluster 9")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, bicluster 1")
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, bicluster 2")
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, bicluster 3")## Warning: ggrepel: 26 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, bicluster 4")## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, bicluster 6")## Warning: ggrepel: 65 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, bicluster 7")
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, bicluster 8")## Warning: ggrepel: 46 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, bicluster 9")
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, bicluster 1")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, bicluster 2")
goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, bicluster 3")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, bicluster 4")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, bicluster 6")
goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, bicluster 7")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, bicluster 8")
goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, bicluster 9")
3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_superbiclust.fabia_mofa.rds")